Secondary Indexes

Hi experts,

I need to have an opinion on the following for performance tuning.

Actually a report was taking long time fetching entries from the tables, so secondary index are created for BSAD, BSID, BSAK and BSIK tables, and reduced the time from 8 hours to 2 hours by this secondary index.

Now becuase of this index, the other processes are getting hampered like a job in BW, uses the same tables. earlier it used to run in 5-10 mins it is now taking around 45-50 mins to run sometimes 2 hours to run.

So how can we improve without hampering any processes?

Thanks,

Rashmi